KISTI Pathway project

Background

The construction of detailed, machine-readable models of
biomolecular pathways is a major goal of systems biology, and
hundreds of models capturing the physical entities and reactions
involved in various pathways are already available from repositories
such as the
BioModels Database
and the
PANTHER Pathway
repository.

However, the manual construction, quality control and maintainance
of pathway models is a demanding and expensive effort, and one of
the key challenges in this effort is the information overload
caused by the exponential growth of the biomedical scientific
literature: currently, a new citation is added into the PubMed
literature database on average once every 40 seconds.

Biomedical text mining systems are increasingly capable of creating
rich structured representations of information automatically
extracted from literature. Such text mining systems open many
opportunities for supporting the curation, validation, and
updating of pathway models.

Building on
the PathText text
mining integration technology for pathways, text mining systems
such as
MEDIE,
event extraction tools such as
EventMine, we are
developing methods for identifying literature relevant to specific
reactions in pathway models and for automatically analysing
documents to extract event structures that capture the full
semantics of pathway reactions.

Visualization of simple event capturing a statement of binding between Whi3 and Cdc28
(from PMID 14685274).

Key among the aims of the project are the development of advanced
ranking technology for determining the relevance of documents to
given pathway reactions and the extension of the scope of event
extraction resources and methods to fully capture the semantics of
statements relevant to biomolecular pathways.

Supporting Tools

BioNLP 2013 Shared Task

To encourage the development of event extraction technology
capable of pathway model curation support tasks, we are organizing
the Pathway Curation event extraction task as part of the upcoming
BioNLP Shared Task 2013.

We will provide task participants with documents relevant to
reactions in a variety of signaling and metabolic pathways and full
manual event annotation for these documents for use in the training
and evaluation of event extraction methods. Please see
the BioNLP Shared task 2013
page for more information and updates.